› 4v1a

Electron Microscopy
3.4Å resolution

Structure of the large subunit of the mammalian mitoribosome, part 2 of 2

Released:
DOI: 10.2210/pdb4v1a/pdb
PDB entry 4v1a coloured by chain, front view.
PDB entry 4v1a coloured by chain, side view.
PDB entry 4v1a coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
The complete structure of the large subunit of the mammalian mitochondrial ribosome.
Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N
Nature 515 283-6 (2014)
PMID: 25271403
Related structures: EMD-2787

Function and Biology Details

Reaction catalysed: 
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 23-mer (preferred)
PDBe Complex ID:
PDB-CPX-102652 (preferred)
Entry contents:
23 distinct polypeptide molecules
Macromolecules (23 distinct):
MITORIBOSOMAL PROTEIN ML37, MRPL37 Chain: a
Molecule details ›
Chain: a
Length: 423 amino acids
Theoretical weight: 47.94 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein mL38 Chain: b
Molecule details ›
Chain: b
Length: 380 amino acids
Theoretical weight: 44.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RW03 (Residues: 1-380; Coverage: 100%)
Gene name: MRPL38
Sequence domains: Phosphatidylethanolamine-binding protein
TGS domain-containing protein Chain: c
Molecule details ›
Chain: c
Length: 334 amino acids
Theoretical weight: 38.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SHP6 (Residues: 1-303, 304-318; Coverage: 100%)
Gene name: MRPL39
MITORIBOSOMAL PROTEIN ML40, MRPL40 Chain: d
Molecule details ›
Chain: d
Length: 206 amino acids
Theoretical weight: 24.08 KDa
Source organism: Sus scrofa
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
MITORIBOSOMAL PROTEIN ML41, MRPL41 Chain: e
Molecule details ›
Chain: e
Length: 135 amino acids
Theoretical weight: 15.07 KDa
Source organism: Sus scrofa
MITORIBOSOMAL PROTEIN ML42, MRPL42 Chain: f
Molecule details ›
Chain: f
Length: 142 amino acids
Theoretical weight: 15.91 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein mL43 Chain: g
Molecule details ›
Chain: g
Length: 159 amino acids
Theoretical weight: 17.73 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S8U4 (Residues: 1-159; Coverage: 100%)
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Structure domains: Glutaredoxin
Large ribosomal subunit protein mL44 Chain: h
Molecule details ›
Chain: h
Length: 332 amino acids
Theoretical weight: 37.53 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SR64 (Residues: 1-332; Coverage: 100%)
Gene name: MRPL44
MITORIBOSOMAL PROTEIN ML45, MRPL45 Chain: i
Molecule details ›
Chain: i
Length: 312 amino acids
Theoretical weight: 36.12 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein mL46 Chain: j
Molecule details ›
Chain: j
Length: 279 amino acids
Theoretical weight: 32.22 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SRT0 (Residues: 1-279; Coverage: 100%)
Gene name: MRPL46
Sequence domains: 39S mitochondrial ribosomal protein L46
Small ribosomal subunit protein uS10 domain-containing protein Chain: k
Molecule details ›
Chain: k
Length: 212 amino acids
Theoretical weight: 23.75 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480J9Z6 (Residues: 58-269; Coverage: 79%)
Gene name: MRPL48
Sequence domains: Ribosomal protein S10p/S20e
Mitochondrial ribosomal protein L18 Chain: l
Molecule details ›
Chain: l
Length: 166 amino acids
Theoretical weight: 18.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0R4J8D5 (Residues: 146-150, 151-163; Coverage: 11%)
Gene name: MRPL18
Structure domains: SUI1-like domain
Large ribosomal subunit protein mL50 Chain: m
Molecule details ›
Chain: m
Length: 159 amino acids
Theoretical weight: 18.35 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3L9H6 (Residues: 40-198; Coverage: 80%)
Gene name: MRPL50
Sequence domains: Ribosomal subunit 39S
MITORIBOSOMAL PROTEIN ML51, MRPL51 Chain: n
Molecule details ›
Chain: n
Length: 128 amino acids
Theoretical weight: 15.22 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein mL52 Chain: o
Molecule details ›
Chain: o
Length: 124 amino acids
Theoretical weight: 13.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S9B7 (Residues: 38-47, 48-160; Coverage: 77%)
Gene name: MRPL52
Sequence domains: Mitoribosomal protein mL52
MITORIBOSOMAL PROTEIN ML53, MRPL53 Chain: p
Molecule details ›
Chain: p
Length: 112 amino acids
Theoretical weight: 12.02 KDa
Source organism: Sus scrofa
Structure domains: Glutaredoxin
MITORIBOSOMAL PROTEIN ML54, MRPL54 Chain: q
Molecule details ›
Chain: q
Length: 138 amino acids
Theoretical weight: 15.96 KDa
Source organism: Sus scrofa
MITORIBOSOMAL PROTEIN ML63, MRPL57, MRP63 Chain: t
Molecule details ›
Chain: t
Length: 102 amino acids
Theoretical weight: 12 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein mL62 Chain: u
Molecule details ›
Chain: u
Length: 205 amino acids
Theoretical weight: 23.28 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: W5IDC0 (Residues: 1-205; Coverage: 100%)
Sequence domains: RF-1 domain
MITORIBOSOMAL PROTEIN ML64, MRPL59, CRIF1 Chain: v
Molecule details ›
Chain: v
Length: 222 amino acids
Theoretical weight: 25.35 KDa
Source organism: Sus scrofa
Structure domains: Growth arrest and DNA-damage-inducible proteins-interacting protein 1
MITORIBOSOMAL PROTEIN ML65, MRPS30 Chain: w
Molecule details ›
Chain: w
Length: 433 amino acids
Theoretical weight: 49.07 KDa
Source organism: Sus scrofa
Mitochondrial ribosomal protein S18A Chain: x
Molecule details ›
Chain: x
Length: 196 amino acids
Theoretical weight: 22.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RRH6 (Residues: 9-25, 26-181; Coverage: 95%)
Gene name: MRPS18A
Sequence domains: Ribosomal protein S18
UNASSIGNED SECONDARY STRUCTURE ELEMENTS Chain: z
Molecule details ›
Chain: z
Length: 47 amino acids
Theoretical weight: 4.02 KDa
Source organism: Sus scrofa

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-2787

Quick links

Citations

49 review citations

Organization and Regulation of Mitochondrial Protein Synthesis.
Ott et al. (2016)
48 more

4 mentions without citation

The 55S mammalian mitochondrial ribosome and its tRNA-exit region.
Kaushal et al. (2015)
3 more